2cym - Revision history

OCA at 09:18, 14 February 2024

2024-02-14T09:18:33Z

←Older revision		Revision as of 09:18, 14 February 2024
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	<StructureSection load='2cym' size='340' side='right'caption='[[2cym]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2cym' size='340' side='right'caption='[[2cym]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_29579 Atcc 29579~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CYM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [https://pdbe.org/2cym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [https://www.ebi.ac.uk/pdbsum/2cym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cym ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [https://pdbe.org/2cym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [https://www.ebi.ac.uk/pdbsum/2cym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cym ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CYC3_DESVH CYC3_DESVH]] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.	+	[https://www.uniprot.org/uniprot/CYC3_DESVH CYC3_DESVH] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2cym ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2cym ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The three-dimensional structure of cytochrome c3 from Desulfovibrio vulgaris Hildenborough has been determined by use of the molecular replacement method and refined at 2.0 A resolution. A suitable crystal of the cytochrome c3 was obtained from buffer solution (25 mM Tris-HCl, pH 7.4), with 75% ethanol as the precipitating reagent. Crystallographic data are as follows: a = 43.17 A, b = 62.91 A, c = 41.17 A, orthorhombic, P2(1)2(1)2(1) and Z = 4. Constrained least-squares refinement and a molecular dynamics procedure with a simulated structure annealing method yielded a crystallographic R-factor of 0.212. The similarity in the folding pattern of both cytochromes c3 is established, the mean deviation of the polypeptide backbone between the two structures being 0.367 A. Most of the amino acids substitutions from DvMF were located on the surface of the molecule, and in particular, S27 and V86 were placed near the propionic acid of the heme group so as to hang over the heme and the cleft of the molecule.
-
-	Effects of amino acid substitution on three-dimensional structure: an X-ray analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 2 A resolution.,Morimoto Y, Tani T, Okumura H, Higuchi Y, Yasuoka N J Biochem. 1991 Oct;110(4):532-40. PMID:1663945<ref>PMID:1663945</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2cym" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]		*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 29579~~]]	+	[[Category: Desulfovibrio vulgaris]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Higuchi, Y]]	+	[[Category: Higuchi Y]]
-	[[Category: Morimoto, Y]]	+	[[Category: Morimoto Y]]
-	[[Category: Okumura, H]]	+	[[Category: Okumura H]]
-	[[Category: Tani, T]]	+	[[Category: Tani T]]
-	[[Category: Yasuoka, N]]	+	[[Category: Yasuoka N]]
-	~~[[Category: Electron transport~~]]	+

OCA at 10:23, 8 December 2021

2021-12-08T10:23:59Z

←Older revision		Revision as of 10:23, 8 December 2021
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	<StructureSection load='2cym' size='340' side='right'caption='[[2cym]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2cym' size='340' side='right'caption='[[2cym]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2CYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CYM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [~~http~~://pdbe.org/2cym PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2cym PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2cym ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [https://pdbe.org/2cym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [https://www.ebi.ac.uk/pdbsum/2cym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cym ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CYC3_DESVH CYC3_DESVH]] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.	+	[[https://www.uniprot.org/uniprot/CYC3_DESVH CYC3_DESVH]] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:33, 4 March 2020

2020-03-04T07:33:42Z

←Older revision		Revision as of 07:33, 4 March 2020
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	==EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION==		==EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION==
-	<StructureSection load='2cym' size='340' side='right' caption='[[2cym]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='2cym' size='340' side='right'caption='[[2cym]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CYM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CYM FirstGlance]. <br>
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Cytochrome c\|Cytochrome c]]	+	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 29579]]		[[Category: Atcc 29579]]
		+	[[Category: Large Structures]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Morimoto, Y]]		[[Category: Morimoto, Y]]

OCA at 06:12, 30 May 2018

2018-05-30T06:12:25Z

←Older revision		Revision as of 06:12, 30 May 2018
Line 1:		Line 1:
		+
	==EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION==		==EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION==
	<StructureSection load='2cym' size='340' side='right' caption='[[2cym]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2cym' size='340' side='right' caption='[[2cym]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CYM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CYM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [http://pdbe.org/2cym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [http://www.ebi.ac.uk/pdbsum/2cym PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [http://pdbe.org/2cym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [http://www.ebi.ac.uk/pdbsum/2cym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2cym ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cy/2cym_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cy/2cym_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2cym ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:53, 11 September 2015

2015-09-11T11:53:11Z

←Older revision		Revision as of 11:53, 11 September 2015
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	<StructureSection load='2cym' size='340' side='right' caption='[[2cym]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2cym' size='340' side='right' caption='[[2cym]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Desulfovibrio_vulgaris Desulfovibrio vulgaris~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CYM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [http://www.ebi.ac.uk/pdbsum/2cym PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [http://pdbe.org/2cym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [http://www.ebi.ac.uk/pdbsum/2cym PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2cym" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desulfovibrio vulgaris~~]]	+	[[Category: Atcc 29579]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Morimoto, Y]]		[[Category: Morimoto, Y]]

OCA at 16:06, 25 December 2014

2014-12-25T16:06:14Z

←Older revision		Revision as of 16:06, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CYM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CYM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [http://www.ebi.ac.uk/pdbsum/2cym PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [http://www.ebi.ac.uk/pdbsum/2cym PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CYC3_DESVH CYC3_DESVH]] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
-	[[Category: Higuchi, Y.]]	+	[[Category: Higuchi, Y]]
-	[[Category: Morimoto, Y.]]	+	[[Category: Morimoto, Y]]
-	[[Category: Okumura, H.]]	+	[[Category: Okumura, H]]
-	[[Category: Tani, T.]]	+	[[Category: Tani, T]]
-	[[Category: Yasuoka, N.]]	+	[[Category: Yasuoka, N]]
	[[Category: Electron transport]]		[[Category: Electron transport]]

OCA at 03:21, 29 September 2014

2014-09-29T03:21:27Z

←Older revision		Revision as of 03:21, 29 September 2014
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-	[[~~Image~~:2cym.~~png\|left~~\|200px]]	+	==EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION==
		+	<StructureSection load='2cym' size='340' side='right' caption='[[2cym]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2cym]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CYM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cym RCSB], [http://www.ebi.ac.uk/pdbsum/2cym PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cy/2cym_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The three-dimensional structure of cytochrome c3 from Desulfovibrio vulgaris Hildenborough has been determined by use of the molecular replacement method and refined at 2.0 A resolution. A suitable crystal of the cytochrome c3 was obtained from buffer solution (25 mM Tris-HCl, pH 7.4), with 75% ethanol as the precipitating reagent. Crystallographic data are as follows: a = 43.17 A, b = 62.91 A, c = 41.17 A, orthorhombic, P2(1)2(1)2(1) and Z = 4. Constrained least-squares refinement and a molecular dynamics procedure with a simulated structure annealing method yielded a crystallographic R-factor of 0.212. The similarity in the folding pattern of both cytochromes c3 is established, the mean deviation of the polypeptide backbone between the two structures being 0.367 A. Most of the amino acids substitutions from DvMF were located on the surface of the molecule, and in particular, S27 and V86 were placed near the propionic acid of the heme group so as to hang over the heme and the cleft of the molecule.

-	~~{{STRUCTURE_2cym\| PDB=2cym \| SCENE= }}~~	+	Effects of amino acid substitution on three-dimensional structure: an X-ray analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 2 A resolution.,Morimoto Y, Tani T, Okumura H, Higuchi Y, Yasuoka N J Biochem. 1991 Oct;110(4):532-40. PMID:1663945<ref>PMID:1663945</ref>

-	~~===EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_1663945}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2cym]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA].~~	+

	==See Also==		==See Also==
	*[[Cytochrome c\|Cytochrome c]]		*[[Cytochrome c\|Cytochrome c]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:001663945<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
	[[Category: Higuchi, Y.]]		[[Category: Higuchi, Y.]]

OCA at 18:42, 20 October 2012

2012-10-20T18:42:17Z

←Older revision		Revision as of 18:42, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[2cym]] is a 1 chain structure ~~of [[Cytochrome c]]~~ with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA].	+	[[2cym]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA].

	==See Also==		==See Also==

OCA: Protected "2cym" [edit=sysop:move=sysop]

2012-07-27T04:57:21Z

Protected "2cym" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:57, 27 July 2012

OCA at 04:57, 27 July 2012

2012-07-27T04:57:20Z

←Older revision		Revision as of 04:57, 27 July 2012
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-	{{Seed}}
	[[Image:2cym.png\|left\|200px]]		[[Image:2cym.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2cym", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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	{{STRUCTURE_2cym\| PDB=2cym \| SCENE= }}		{{STRUCTURE_2cym\| PDB=2cym \| SCENE= }}

	===EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION===		===EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_1663945}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 1663945 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_1663945}}		{{ABSTRACT_PUBMED_1663945}}

	==About this Structure==		==About this Structure==
-	~~2CYM~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA].	+	[[2cym]] is a 1 chain structure of [[Cytochrome c]] with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYM OCA].
		+
		+	==See Also==
		+	*[[Cytochrome c\|Cytochrome c]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~1663945~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:001663945</ref><references group="xtra"/>
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
	[[Category: Higuchi, Y.]]		[[Category: Higuchi, Y.]]
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	[[Category: Yasuoka, N.]]		[[Category: Yasuoka, N.]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:17:33 2009''